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Sample GSM195220 Query DataSets for GSM195220
Status Public on Jun 30, 2007
Title stigma 3, biological rep 2
Sample type RNA
 
Source name mature stigmas
Organism Oryza sativa
Characteristics genotype: Japonica Nipponbare
age: unpollinated stigmas at anthesis
age: rice stigma before pollination
Growth protocol natural conditions,growing season begins from December to next April, in an experimental farm in Hainan, China.
Extracted molecule total RNA
Extraction protocol remove lemma and palea from floret, the stigma is extracted by cutting the pistil just below the base of the plumose stigma
total RNA was isolated and purified by Qiagen RNeasy kit
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 degree on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Description Gene expression data from rice stigma
Data processing The data were analyzed with GCOS software (Microarray Suite version 5.0, MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
 
Submission date May 29, 2007
Last update date Jul 31, 2009
Contact name Wenying Xu
E-mail(s) wyxu@genetics.ac.cn
Organization name Institute of Genetics and Developmental Biology of the Chinese Academy of Sciences
Street address Datun Road, Chaoyang District
City Beijing
ZIP/Postal code 100101
Country China
 
Platform ID GPL2025
Series (1)
GSE7951 Genome-wide gene expression profiling of rice stigma

Data table header descriptions
ID_REF
VALUE MAS5-calculated Signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 416.4 P 0.000754
AFFX-BioB-M_at 467.5 P 0.00006
AFFX-BioB-3_at 295.4 P 0.00007
AFFX-BioC-5_at 695.6 P 0.000052
AFFX-BioC-3_at 734.8 P 0.000044
AFFX-BioDn-5_at 2795.6 P 0.000044
AFFX-BioDn-3_at 6556.7 P 0.000052
AFFX-CreX-5_at 17362.1 P 0.000052
AFFX-CreX-3_at 20950 P 0.000044
AFFX-DapX-5_at 362.3 P 0.000095
AFFX-DapX-M_at 846.5 P 0.000581
AFFX-DapX-3_at 1216.5 P 0.00007
AFFX-LysX-5_at 65 P 0.00034
AFFX-LysX-M_at 136.9 A 0.239063
AFFX-LysX-3_at 388.1 P 0.000095
AFFX-PheX-5_at 77.9 P 0.004017
AFFX-PheX-M_at 95.7 P 0.004017
AFFX-PheX-3_at 216.6 P 0.004017
AFFX-ThrX-5_at 100.5 P 0.028457
AFFX-ThrX-M_at 152.1 P 0.000225

Total number of rows: 57381

Table truncated, full table size 1956 Kbytes.




Supplementary file Size Download File type/resource
GSM195220.CEL.gz 4.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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